R/print.est.data.frame.R

In nonrandom: Stratification and matching by the propensity score

print.est.data.frame <- function(x,
                                 ...)
{

  object <- x
  
  cat("\n Effect estimation for treatment/exposure on outcome \n")
  cat("\n Treatment/exposure:", object$name.treat)
  cat("\n Outcome:", object$name.resp)
  
  if( object$family == "binomial" ){
    cat("\n Effect measure: odds ratio ('or')\n\n")
    col.n <- c("or","SE[log[or]]","[95%-CI[or]]")
  }else{
    cat("\n Effect measure: difference ('effect')\n\n")
    col.n <- c("effect","SE[effect]","[95%-CI[effect]]")
  }
  
  if ( !is.list(object$lr.estimation) ){
    lr.eff.c <- lr.se.c <- NULL
    lr.eff.m <- lr.se.m <- NULL
    lr.ci.c <- lr.ci.m <- NULL
    
  }else{
    if( object$family == "binomial" ){
      lr.eff.c <- round(object$lr.estimation$effect,3)
      lr.se.c  <- round(object$lr.estimation$se,4)
      lr.eff.m <- round(object$lr.estimation$effect.marg,3)
      lr.se.m  <- round(object$lr.estimation$se.marg,4)

      lr.ci.c <- round(c(exp(log(lr.eff.c) - qnorm(0.975)*lr.se.c),
                         exp(log(lr.eff.c) + qnorm(0.975)*lr.se.c)),3)

      lr.ci.m <- round(c(exp(log(lr.eff.m) - qnorm(0.975)*lr.se.m),
                         exp(log(lr.eff.m) + qnorm(0.975)*lr.se.m)),3)
    }else{
      lr.eff.c <- round(object$lr.estimation$effect,3)
      lr.se.c  <- round(object$lr.estimation$se,4)
      
      lr.ci.c <- round(c(lr.eff.c - qnorm(0.975)*lr.se.c,
                         lr.eff.c + qnorm(0.975)*lr.se.c),3)
    }
  }
    
  if ( !is.list(object$ps.estimation$adj) ){    
    ps.adj.eff <-
      ps.adj.se <-
        ps.adj.ci <- NULL
  }else{
    ps.adj.eff <- round(object$ps.estimation$adj$effect,3)
    ps.adj.se  <- round(object$ps.estimation$adj$se,4)
    
    if( object$family == "binomial" ){
      ps.adj.ci <- round(c(exp(log(ps.adj.eff) - qnorm(0.975)*ps.adj.se),
                           exp(log(ps.adj.eff) + qnorm(0.975)*ps.adj.se)),3)     
    }else{
      ps.adj.ci <- round(c(ps.adj.eff - qnorm(0.975)*ps.adj.se,
                           ps.adj.eff + qnorm(0.975)*ps.adj.se),3)     
    }
  }
  
  if ( object$family=="binomial" ){

    crude <- round(object$ps.estimation$crude$effect,3)
    crude.se <- round(object$ps.estimation$crude$se,4)
    crude.ci <- round(c(exp(log(crude)-qnorm(0.975)*crude.se),
                        exp(log(crude)+qnorm(0.975)*crude.se)),3)

    if (!is.null(object$stratum.index)){
    
      rr <- round(object$ps.estimation$unadj$effect,3)
      rr.se <- round(object$ps.estimation$unadj$se,4)  
      mh <- round(object$ps.estimation$unadj$effect.mh,3)
      mh.se <- round(object$ps.estimation$unadj$se.mh,4)
      
      rr.ci <- round(c(exp(log(rr)-qnorm(0.975)*rr.se),
                       exp(log(rr)+qnorm(0.975)*rr.se)),3)
      mh.ci <- round(c(exp(log(mh)-qnorm(0.975)*mh.se),
                       exp(log(mh)+qnorm(0.975)*mh.se)),3)
    }else{

      diff <- round(object$ps.estimation$unadj$effect,3)
      diff.se <- round(object$ps.estimation$unadj$se,4)  
      
      diff.ci <- round(c(exp(log(diff)-qnorm(0.975)*diff.se),
                         exp(log(diff)+qnorm(0.975)*diff.se)),3)      
    }
  }else{
    
    crude <- round(object$ps.estimation$crude$effect,3)
    crude.se <- round(object$ps.estimation$crude$se,4)
    crude.ci <- round(c(crude-qnorm(0.975)*crude.se,
                        crude+qnorm(0.975)*crude.se),3)
    
    diff <- round(object$ps.estimation$unadj$effect,3)
    diff.se <- round(object$ps.estimation$unadj$se,4) 
    diff.ci <- round(c(diff-qnorm(0.975)*diff.se,
                       diff+qnorm(0.975)*diff.se),3)
  }
  

  if ( object$family=="binomial" ){

    if ( !is.null(object$stratum.index) ){ 

      eff <- c(" -----",
               paste("",crude,sep=""),
               "",
               paste("",rr,sep=""),
               paste("",mh,sep=""),
               paste("",ps.adj.eff,sep=""),
               "",
               paste("",lr.eff.c,sep=""),
               paste("",lr.eff.m,sep=""),
               "")
      
      se <- c(" -----------",
              paste("",crude.se,"", sep=""),
              "",
              paste("",rr.se,"", sep=""),
              paste("",mh.se,"", sep=""),
              paste("",ps.adj.se,"", sep=""),
              "",
              paste("",lr.se.c,"", sep=""),
              paste("",lr.se.m,"", sep=""),
              "")
      
      ci <- c(" ------------",
              paste("[",crude.ci[1],",",crude.ci[2], "]",sep=""),
              "",
              paste("[",rr.ci[1],",",rr.ci[2],"]",sep=""),
              paste("[",mh.ci[1],",",mh.ci[2],"]",sep=""),
              paste("[",ps.adj.ci[1],",",ps.adj.ci[2],"]",sep=""),
              "",
              paste("[",lr.ci.c[1],",",lr.ci.c[2],"]",sep=""),
              paste("[",lr.ci.m[1],",",lr.ci.m[2],"]",sep=""),
              "")
      
    df <- data.frame(cbind(eff, se, ci),
                     row.names=c("",
                       "Crude",
                       "Stratification", "  Outcome rates", "  MH", "  Adjusted",
                       "Regression", "  Conditional", "  Marginal", " "))

    }else{
      
      eff <- c(" ------",
               paste("",crude,sep=""),
               "",
               paste("",diff,sep=""),
               paste("",ps.adj.eff,sep=""),
               "",
               paste("",lr.eff.c,sep=""),
               paste("",lr.eff.m,sep=""),
               "")
      
      se <- c(" ----------",
              paste("",crude.se,"", sep=""),
              "",
              paste("",diff.se,"", sep=""),
              paste("",ps.adj.se,"", sep=""),
              "",
              paste("",lr.se.c,"", sep=""),
              paste("",lr.se.m,"", sep=""),
              "")
      
      ci <- c(" ----------------",
              paste("[",crude.ci[1],",",crude.ci[2], "]",sep=""),
              "",
              paste("[",diff.ci[1],",",diff.ci[2],"]",sep=""),
              paste("[",ps.adj.ci[1],",",ps.adj.ci[2],"]",sep=""),
              "",
              paste("[",lr.ci.c[1],",",lr.ci.c[2],"]",sep=""),
              paste("[",lr.ci.m[1],",",lr.ci.m[2],"]",sep=""),
              "")
      
      df <- data.frame(cbind(eff, se, ci),
                       row.names=c("",
                         "Crude",
                         "Matching", " Unadjusted", " Adjusted",
                         "Regression", "  Conditional", "  Marginal", " "))
      
    }
    colnames(df) <- col.n
    
  }else{ ## gaussian
    
    eff <- c(" ------",
             paste("",crude,sep=""),
             "",
             paste("",diff,sep=""),
             paste("",ps.adj.eff,sep=""),
             paste("",lr.eff.c,sep=""),
             "")
    
    se <- c(" ----------",
            paste("",crude.se,"", sep=""),
            "",
            paste("",diff.se,"", sep=""),
            paste("",ps.adj.se,"", sep=""),
            paste("",lr.se.c,"", sep=""),
            "")
    
    ci <- c(" ----------------",
            paste("[",crude.ci[1],",",crude.ci[2], "]",sep=""),
            "",
            paste("[",diff.ci[1],",",diff.ci[2],"]",sep=""),
            paste("[",ps.adj.ci[1],",",ps.adj.ci[2],"]",sep=""),
            paste("[",lr.ci.c[1],",",lr.ci.c[2],"]",sep=""),
            "")

    if ( !is.null(object$stratum.index) ){ ## stratified
    
      df <- data.frame(cbind(eff, se, ci),
                       row.names=c("",
                         "Crude",
                         "Stratification", " Unadjusted", " Adjusted",
                         "Regression", " "))

    }else{ ## matched
      
      df <- data.frame(cbind(eff, se, ci),
                       row.names=c("",
                         "Crude",
                         "Matching", " Unadjusted", " Adjusted",
                         "Regression", " "))
    }
    colnames(df) <- col.n 
  }
  cat("\n Table of effect estimates:\n\n")  
  print(format(df))  
}